<!doctype html>
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<meta charset='UTF-8'><meta name='viewport' content='width=device-width initial-scale=1'>
<title>3 基因注释</title><style type='text/css'>html {overflow-x: initial !important;}#write, body { height: auto; }
#write, #write h1, #write h2, #write h3, #write h4, #write h5, #write h6, #write ol, #write p, #write ul { position: relative; }
#write, #write h1, #write h2, #write h3, #write h4, #write h5, #write h6, #write p, #write pre { width: inherit; }
#write, pre { white-space: pre-wrap; }
.CodeMirror, .md-fences, table { text-align: left; }
.md-reset, a:active, a:hover { outline: 0px; }
.md-reset, .md-toc-item a { text-decoration: none; }
.MathJax_SVG, .md-reset { float: none; direction: ltr; }
:root { --bg-color:#ffffff; --text-color:#333333; }
html { font-size: 14px; background-color: var(--bg-color); color: var(--text-color); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; -webkit-font-smoothing: antialiased; }
body { margin: 0px; padding: 0px; bottom: 0px; top: 0px; left: 0px; right: 0px; font-size: 1rem; line-height: 1.42857; overflow-x: hidden; background: inherit; }
a.url { word-break: break-all; }
.in-text-selection, ::selection { background: rgb(181, 214, 252); text-shadow: none; }
#write { margin: 0px auto; word-break: normal; word-wrap: break-word; padding-bottom: 70px; overflow-x: visible; }
.first-line-indent #write p .md-line { text-indent: 0px; }
.first-line-indent #write li, .first-line-indent #write p, .first-line-indent #write p .md-line:first-child { text-indent: 2em; }
.for-image #write { padding-left: 8px; padding-right: 8px; }
body.typora-export { padding-left: 30px; padding-right: 30px; }
@media screen and (max-width: 500px) {
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  .CodeMirror-gutters { display: none !important; }
}
#write > blockquote:first-child, #write > div:first-child, #write > ol:first-child, #write > p:first-child, #write > pre:first-child, #write > table:first-child, #write > ul:first-child { margin-top: 30px; }
#write li > table:first-child { margin-top: -20px; }
img { max-width: 100%; vertical-align: middle; }
button, input, select, textarea { color: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; }
input[type="checkbox"], input[type="radio"] { line-height: normal; padding: 0px; }
*, ::after, ::before { box-sizing: border-box; }
h1 { font-size: 2rem; }
h2 { font-size: 1.8rem; }
h3 { font-size: 1.6rem; }
h4 { font-size: 1.4rem; }
h5 { font-size: 1.2rem; }
h6 { font-size: 1rem; }
p { -webkit-margin-before: 1rem; -webkit-margin-after: 1rem; -webkit-margin-start: 0px; -webkit-margin-end: 0px; }
.mathjax-block { margin-top: 0px; margin-bottom: 0px; -webkit-margin-before: 0px; -webkit-margin-after: 0px; }
.hidden { display: none; }
.md-blockmeta { color: rgb(204, 204, 204); font-weight: 700; font-style: italic; }
a { cursor: pointer; }
sup.md-footnote { padding: 2px 4px; background-color: rgba(238, 238, 238, 0.7); color: rgb(85, 85, 85); border-radius: 4px; }
#write input[type="checkbox"] { cursor: pointer; width: inherit; height: inherit; }
#write > figure:first-child { margin-top: 16px; }
figure { overflow-x: auto; margin: -8px 0px 0px -8px; max-width: calc(100% + 16px); padding: 8px; }
tr { break-inside: avoid; break-after: auto; }
thead { display: table-header-group; }
table { border-collapse: collapse; border-spacing: 0px; width: 100%; overflow: auto; break-inside: auto; }
.CodeMirror-line, .md-fences { break-inside: avoid; }
table.md-table td { min-width: 80px; }
.CodeMirror-gutters { border-right: 0px; background-color: inherit; margin-right: 4px; }
.CodeMirror-placeholder { opacity: 0.3; }
.CodeMirror pre { padding: 0px 4px; }
.CodeMirror-lines { padding: 0px; }
div.hr:focus { cursor: none; }
.md-fences { font-size: 0.9rem; display: block; overflow: visible; white-space: pre; background: inherit; position: relative !important; }
.md-diagram-panel { width: 100%; margin-top: 10px; text-align: center; padding-top: 0px; padding-bottom: 8px; overflow-x: auto; }
.md-fences .CodeMirror.CodeMirror-wrap { top: -1.6em; margin-bottom: -1.6em; }
.md-fences.mock-cm { white-space: pre-wrap; }
.show-fences-line-number .md-fences { padding-left: 0px; }
.show-fences-line-number .md-fences.mock-cm { padding-left: 40px; }
.footnotes { opacity: 0.8; font-size: 0.9rem; margin-top: 1em; margin-bottom: 1em; }
.footnotes + .footnotes { margin-top: 0px; }
.md-reset { margin: 0px; padding: 0px; border: 0px; vertical-align: top; background: 0px 0px; text-shadow: none; position: static; width: auto; height: auto; white-space: nowrap; cursor: inherit; -webkit-tap-highlight-color: transparent; line-height: normal; font-weight: 400; text-align: left; box-sizing: content-box; }
.md-toc-inner, a img, img a { cursor: pointer; }
li div { padding-top: 0px; }
blockquote { margin: 1rem 0px; }
li .mathjax-block, li p { margin: 0.5rem 0px; }
li { margin: 0px; position: relative; }
blockquote > :last-child { margin-bottom: 0px; }
blockquote > :first-child { margin-top: 0px; }
.footnotes-area { color: rgb(136, 136, 136); margin-top: 0.714rem; padding-bottom: 0.143rem; white-space: normal; }
@media print {
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  h1, h2, h3, h4, h5, h6 { break-after: avoid-page; orphans: 2; }
  p { orphans: 4; }
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  .typora-export #write { padding-left: 1cm; padding-right: 1cm; padding-bottom: 0px; break-after: avoid; }
  .typora-export #write::after { height: 0px; }
  @page { margin: 20mm 0px; }
}
.footnote-line { white-space: pre-wrap; margin-top: 0.714em; font-size: 0.7em; }
pre.md-meta-block { font-size: 0.8rem; min-height: 0.8rem; white-space: pre-wrap; background: rgb(204, 204, 204); display: block; overflow-x: hidden; }
p > img:only-child { display: block; margin: auto; }
.md-line > .md-image:only-child, p > .md-image:only-child { display: inline-block; width: 100%; text-align: center; }
.mathjax-block:not(:empty)::after, .md-toc-content::after, .md-toc::after { display: none; }
#write .MathJax_Display { margin: 0.8em 0px 0px; }
.mathjax-block { white-space: pre; overflow: hidden; width: 100%; }
p + .mathjax-block { margin-top: -1.143rem; }
[contenteditable="true"]:active, [contenteditable="true"]:focus { outline: 0px; box-shadow: none; }
.md-task-list-item { position: relative; list-style-type: none; }
.task-list-item.md-task-list-item { padding-left: 0px; }
.md-task-list-item > input { position: absolute; top: 0px; left: 0px; margin-left: -1.2em; margin-top: calc(1em - 10px); }
.math { font-size: 1rem; }
.md-toc { min-height: 3.58rem; position: relative; font-size: 0.9rem; border-radius: 10px; }
.MathJax_SVG, .mathjax-block .MathJax_SVG_Display { text-indent: 0px; max-width: none; max-height: none; min-height: 0px; }
.md-toc-content { position: relative; margin-left: 0px; }
.md-toc-item { display: block; color: rgb(65, 131, 196); }
.md-toc-inner:hover { }
.md-toc-inner { display: inline-block; }
.md-toc-h1 .md-toc-inner { margin-left: 0px; font-weight: 700; }
.md-toc-h2 .md-toc-inner { margin-left: 2em; }
.md-toc-h3 .md-toc-inner { margin-left: 4em; }
.md-toc-h4 .md-toc-inner { margin-left: 6em; }
.md-toc-h5 .md-toc-inner { margin-left: 8em; }
.md-toc-h6 .md-toc-inner { margin-left: 10em; }
@media screen and (max-width: 48em) {
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  .md-toc-h4 .md-toc-inner { margin-left: 5em; }
  .md-toc-h5 .md-toc-inner { margin-left: 6.5em; }
  .md-toc-h6 .md-toc-inner { margin-left: 8em; }
}
a.md-toc-inner { font-size: inherit; font-style: inherit; font-weight: inherit; line-height: inherit; }
.footnote-line a:not(.reversefootnote) { color: inherit; }
.md-attr { display: none; }
.md-fn-count::after { content: "."; }
code, pre, tt { font-family: var(--monospace); }
.md-comment { color: rgb(162, 127, 3); opacity: 0.8; font-family: var(--monospace); }
code { text-align: left; }
a.md-print-anchor { border-width: initial !important; border-style: none !important; border-color: initial !important; display: inline-block !important; position: absolute !important; width: 1px !important; right: 0px !important; outline: 0px !important; background: 0px 0px !important; text-decoration: initial !important; text-shadow: initial !important; }
.md-inline-math .MathJax_SVG .noError { display: none !important; }
.mathjax-block .MathJax_SVG_Display { text-align: center; margin: 1em 0px; position: relative; min-width: 100%; width: auto; display: block !important; }
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.MathJax_SVG { display: inline; font-style: normal; font-weight: 400; line-height: normal; zoom: 90%; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; min-width: 0px; border: 0px; padding: 0px; margin: 0px; }
.MathJax_SVG * { transition: none; }
.os-windows.monocolor-emoji .md-emoji { font-family: "Segoe UI Symbol", sans-serif; }
.md-diagram-panel > svg, [lang="flow"] svg, [lang="mermaid"] svg { max-width: 100%; }
[lang="mermaid"] .node text { font-size: 1rem; }
table tr th { border-bottom: 0px; }


.CodeMirror, .CodeMirror-sizer { position: relative; }
.CodeMirror.cm-s-inner { background: inherit; }
.fences-no-line-wrapping .md-fences .CodeMirror { margin-top: -20px; }
.CodeMirror-scroll { overflow-y: hidden; overflow-x: auto; }
.CodeMirror-lines { padding: 4px 0px; }
.CodeMirror-gutter-filler, .CodeMirror-scrollbar-filler { background-color: rgb(255, 255, 255); }
.CodeMirror-scroll, .cm-s-inner .CodeMirror-activeline-background { background: inherit; }
.CodeMirror-linenumber { padding: 0px 3px 0px 5px; text-align: right; color: rgb(153, 153, 153); }
.cm-s-inner .cm-keyword { color: rgb(119, 0, 136); }
.cm-s-inner .cm-atom, .cm-s-inner.cm-atom { color: rgb(34, 17, 153); }
.cm-s-inner .cm-number { color: rgb(17, 102, 68); }
.cm-s-inner .cm-def { color: rgb(0, 0, 255); }
.cm-s-inner .cm-variable { color: rgb(0, 0, 0); }
.cm-s-inner .cm-variable-2 { color: rgb(0, 85, 170); }
.cm-s-inner .cm-variable-3 { color: rgb(0, 136, 85); }
.cm-s-inner .cm-string { color: rgb(170, 17, 17); }
.cm-s-inner .cm-property { color: rgb(0, 0, 0); }
.cm-s-inner .cm-operator { color: rgb(152, 26, 26); }
.cm-s-inner .cm-comment, .cm-s-inner.cm-comment { color: rgb(170, 85, 0); }
.cm-s-inner .cm-string-2 { color: rgb(255, 85, 0); }
.cm-s-inner .cm-meta, .cm-s-inner .cm-qualifier { color: rgb(85, 85, 85); }
.cm-s-inner .cm-builtin { color: rgb(51, 0, 170); }
.cm-s-inner .cm-bracket { color: rgb(153, 153, 119); }
.cm-s-inner .cm-tag { color: rgb(17, 119, 0); }
.cm-s-inner .cm-attribute { color: rgb(0, 0, 204); }
.cm-s-inner .cm-header, .cm-s-inner.cm-header { color: rgb(0, 0, 255); }
.cm-s-inner .cm-quote, .cm-s-inner.cm-quote { color: rgb(0, 153, 0); }
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.cm-s-inner .cm-link, .cm-s-inner.cm-link { color: rgb(0, 0, 204); }
.cm-negative { color: rgb(221, 68, 68); }
.cm-positive { color: rgb(34, 153, 34); }
.cm-header, .cm-strong { font-weight: 700; }
.cm-del { text-decoration: line-through; }
.cm-em { font-style: italic; }
.cm-link { text-decoration: underline; }
.cm-error, .cm-invalidchar { color: red; }
.cm-constant { color: rgb(38, 139, 210); }
.cm-defined { color: rgb(181, 137, 0); }
div.CodeMirror span.CodeMirror-matchingbracket { color: rgb(0, 255, 0); }
div.CodeMirror span.CodeMirror-nonmatchingbracket { color: rgb(255, 34, 34); }
.CodeMirror { height: auto; overflow: hidden; }
.CodeMirror-scroll { margin-bottom: -30px; padding-bottom: 30px; height: 100%; outline: 0px; position: relative; box-sizing: content-box; }
.CodeMirror-gutter-filler, .CodeMirror-hscrollbar, .CodeMirror-scrollbar-filler, .CodeMirror-vscrollbar { position: absolute; z-index: 6; display: none; }
.CodeMirror-vscrollbar { right: 0px; top: 0px; overflow-x: hidden; overflow-y: scroll; }
.CodeMirror-hscrollbar { bottom: 0px; left: 0px; overflow-y: hidden; overflow-x: scroll; }
.CodeMirror-scrollbar-filler { right: 0px; bottom: 0px; }
.CodeMirror-gutter-filler { left: 0px; bottom: 0px; }
.CodeMirror-gutters { border-right: 1px solid rgb(221, 221, 221); background: inherit; white-space: nowrap; position: absolute; left: 0px; top: 0px; padding-bottom: 30px; z-index: 3; }
.CodeMirror-gutter { white-space: normal; height: 100%; box-sizing: content-box; padding-bottom: 30px; margin-bottom: -32px; display: inline-block; }
.CodeMirror-gutter-wrapper { position: absolute; z-index: 4; background: 0px 0px !important; border: none !important; }
.CodeMirror-gutter-background { position: absolute; top: 0px; bottom: 0px; z-index: 4; }
.CodeMirror-gutter-elt { position: absolute; cursor: default; z-index: 4; }
.CodeMirror-lines { cursor: text; }
.CodeMirror pre { border-radius: 0px; border-width: 0px; background: 0px 0px; font-family: inherit; font-size: inherit; margin: 0px; white-space: pre; word-wrap: normal; color: inherit; z-index: 2; position: relative; overflow: visible; }
.CodeMirror-wrap pre { word-wrap: break-word; white-space: pre-wrap; word-break: normal; }
.CodeMirror-code pre { border-right: 30px solid transparent; width: fit-content; }
.CodeMirror-wrap .CodeMirror-code pre { border-right: none; width: auto; }
.CodeMirror-linebackground { position: absolute; left: 0px; right: 0px; top: 0px; bottom: 0px; z-index: 0; }
.CodeMirror-linewidget { position: relative; z-index: 2; overflow: auto; }
.CodeMirror-wrap .CodeMirror-scroll { overflow-x: hidden; }
.CodeMirror-measure { position: absolute; width: 100%; height: 0px; overflow: hidden; visibility: hidden; }
.CodeMirror-measure pre { position: static; }
.CodeMirror div.CodeMirror-cursor { position: absolute; border-right: none; width: 0px; visibility: hidden; }
.CodeMirror-focused div.CodeMirror-cursor { visibility: inherit; }
.CodeMirror-selected { background: rgb(217, 217, 217); }
.CodeMirror-focused .CodeMirror-selected { background: rgb(215, 212, 240); }
.cm-searching { background: rgba(255, 255, 0, 0.4); }
@media print {
  .CodeMirror div.CodeMirror-cursor { visibility: hidden; }
}
.CodeMirror-lint-markers { width: 16px; }
.CodeMirror-lint-tooltip { background-color: infobackground; border: 1px solid rgb(0, 0, 0); border-radius: 4px; color: infotext; font-family: var(--monospace); overflow: hidden; padding: 2px 5px; position: fixed; white-space: pre-wrap; z-index: 10000; max-width: 600px; opacity: 0; transition: opacity 0.4s; font-size: 0.8em; }
.CodeMirror-lint-mark-error, .CodeMirror-lint-mark-warning { background-position: left bottom; background-repeat: repeat-x; }
.CodeMirror-lint-mark-error { background-image: url(""); }
.CodeMirror-lint-marker-error, .CodeMirror-lint-marker-warning { background-position: center center; background-repeat: no-repeat; cursor: pointer; display: inline-block; height: 16px; width: 16px; vertical-align: middle; position: relative; }
.CodeMirror-lint-message-error, .CodeMirror-lint-message-warning { padding-left: 18px; background-position: left top; background-repeat: no-repeat; }
.CodeMirror-lint-marker-error, .CodeMirror-lint-message-error { background-image: url(""); }
.CodeMirror-lint-marker-warning, .CodeMirror-lint-message-warning { background-image: url(""); }
.CodeMirror-lint-marker-multiple { background-image: url(""); background-repeat: no-repeat; background-position: right bottom; width: 100%; height: 100%; }


.output_wrapper { font-size: 16px; color: rgb(62, 62, 62); line-height: 1.6; word-spacing: 0px; letter-spacing: 0px; font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif; }
.output_wrapper * { font-size: inherit; color: inherit; line-height: inherit; margin: 0px; padding: 0px; }
p { margin: 1.5em 0px; }
h1, h2, h3, h4, h5, h6 { margin: 1.5em 0px; font-weight: bold; color: rgb(21, 153, 87); }
h1 { font-size: 1.6em; }
h2 { font-size: 1.4em; }
h3 { font-size: 1.3em; }
h4 { font-size: 1.2em; }
h5 { font-size: 1em; }
h6 { font-size: 1em; }
ul, ol { padding-left: 32px; }
ul { list-style-type: disc; }
ol { list-style-type: decimal; }
li * { }
li { margin-bottom: 0.5em; }
.code_size_default { line-height: 18px; font-size: 14px; font-weight: normal; word-spacing: 0px; letter-spacing: 0px; }
.code_size_tight { line-height: 15px; font-size: 11px; font-weight: normal; word-spacing: -3px; letter-spacing: 0px; }
pre code { font-family: Consolas, Inconsolata, Courier, monospace; border-radius: 0px; }
blockquote { display: block; padding: 15px 15px 15px 1rem; font-size: 0.9em; margin: 1em 0px; color: rgb(129, 145, 152); border-left: 6px solid rgb(220, 230, 240); background: rgb(242, 247, 251); overflow: auto; word-wrap: normal; word-break: normal; }
blockquote p { margin: 0px; }
a { text-decoration: none; color: rgb(30, 107, 184); word-wrap: break-word; }
strong { font-weight: bold; }
em { font-style: italic; }
del { font-style: italic; }
strong em { font-weight: bold; }
hr { height: 1px; margin: 1.5rem 0px; border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1px dashed rgb(165, 165, 165); }
code { word-wrap: break-word; padding: 2px 4px; border-radius: 4px; margin: 0px 2px; color: rgb(233, 105, 0); background: rgb(248, 248, 248); }
img { display: block; margin: 0px auto; max-width: 100%; }
figcaption { margin-top: 10px; text-align: center; color: rgb(153, 153, 153); font-size: 0.7em; }
table { display: table; width: 100%; text-align: left; }
tbody { border: 0px; }
table tr { border-width: 1px 0px 0px; border-right-style: initial; border-bottom-style: initial; border-left-style: initial; border-right-color: initial; border-bottom-color: initial; border-left-color: initial; border-image: initial; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: white; }
table tr th, table tr td { font-size: 1em; border: 1px solid rgb(204, 204, 204); padding: 0.5em 1em; text-align: left; }
table tr th { font-weight: bold; background-color: rgb(240, 240, 240); }
.katex-display { font-size: 1.5em; }
a[href^="#"] sup { vertical-align: super; margin: 0px 2px; padding: 1px 3px; color: rgb(255, 255, 255); background: rgb(102, 102, 102); font-size: 0.7em; }
.task-list-list { list-style-type: none; }
.task-list-list.checked { color: rgb(62, 62, 62); }
.task-list-list.uncheck { color: rgb(191, 193, 191); }
.task-list-list .icon_uncheck, .task-list-list .icon_check { display: inline-block; vertical-align: middle; margin-right: 10px; }
.task-list-list .icon_check::before { content: "√"; border: 2px solid rgb(62, 62, 62); color: red; }
.task-list-list .icon_uncheck::before { content: "x"; border: 2px solid rgb(191, 193, 191); color: rgb(191, 193, 191); }
.task-list-list .icon_check::before, .task-list-list .icon_uncheck::before { padding: 2px 8px 2px 5px; border-radius: 5px; }
.toc { margin-left: 25px; }
.toc_item { display: block; }
.toc_left { margin-left: 25px; }
.cm-s-inner.CodeMirror { background: rgb(245, 245, 245); color: rgb(7, 54, 66); }
.cm-s-inner div.CodeMirror-selected { background: rgb(238, 232, 213) !important; }
.cm-s-inner .CodeMirror-gutters { background: rgb(245, 245, 245); border-right: 0px; }
.cm-s-inner .CodeMirror-linenumber { color: rgb(131, 148, 150); }
.cm-s-inner .CodeMirror-cursor { border-left: 1px solid rgb(101, 123, 131) !important; }
.cm-s-inner span.cm-comment { color: rgb(211, 54, 130); }
.cm-s-inner span.cm-atom { color: rgb(108, 113, 196); }
.cm-s-inner span.cm-number { color: rgb(108, 113, 196); }
.cm-s-inner span.cm-property, .cm-s-inner span.cm-attribute { color: rgb(133, 153, 0); }
.cm-s-inner span.cm-keyword { color: rgb(220, 50, 47); }
.cm-s-inner span.cm-string { color: rgb(181, 137, 0); }
.cm-s-inner span.cm-variable { color: rgb(133, 153, 0); }
.cm-s-inner span.cm-variable-2 { color: rgb(38, 139, 210); }
.cm-s-inner span.cm-def { color: rgb(203, 75, 22); }
.cm-s-inner span.cm-error { background: rgb(220, 50, 47); color: rgb(101, 123, 131); }
.cm-s-inner span.cm-bracket { color: rgb(7, 54, 66); }
.cm-s-inner span.cm-tag { color: rgb(220, 50, 47); }
.cm-s-inner span.cm-link { color: rgb(108, 113, 196); }
.cm-s-inner .CodeMirror-matchingbracket { text-decoration: underline; color: white !important; }
.md-fences { background-color: rgb(245, 245, 245); color: rgb(233, 237, 237); border: none; }
.md-fences .code-tooltip { background-color: black; }
#write { max-width: 660px; padding: 20px 15px 15px; }





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<div  id='write'  class = 'is-node'><div class='md-toc' mdtype='toc'><p class="md-toc-content"><span class="md-toc-item md-toc-h2" data-ref="n284"><a class="md-toc-inner" href="#header-n284">3.1 芯片注释-联结基因信息与芯片</a></span><span class="md-toc-item md-toc-h2" data-ref="n11"><a class="md-toc-inner" href="#header-n11">3.2 下载Affymetrix芯片注释信息</a></span><span class="md-toc-item md-toc-h2" data-ref="n146"><a class="md-toc-inner" href="#header-n146">3.3 GO（Gene Ontology）数据库</a></span><span class="md-toc-item md-toc-h3" data-ref="n150"><a class="md-toc-inner" href="#header-n150">3.3.1 基本组成</a></span></p></div><p>&nbsp;</p><h2><a name='header-n284' class='md-header-anchor '></a>3.1 芯片注释-联结基因信息与芯片</h2><p>芯片的注释信息随着对基因认识及序列的改变而更新，Affymetrix公司维护的芯片注释信息每三个月更新一次</p><blockquote><p>假设通过基因芯片，筛选出600个表达有差异的基因，我们想要知道：</p><p>（a）这些基因的变化体现了生物的何种功能的改变</p><p>（b）它们是否通过网络调控关系或在某些生物调控通路中发挥作用</p></blockquote><h2><a name='header-n11' class='md-header-anchor '></a>3.2 下载Affymetrix芯片注释信息</h2><p>首先进入官网<a href='http://www.affymetrix.com' target='_blank' class='url'>http://www.affymetrix.com</a>，免费注册一个账号，登录后，进入网站<a href='http://www.affymetrix.com/support/technical/byproduct.affx' target='_blank' class='url'>http://www.affymetrix.com/support/technical/byproduct.affx</a>，在<code>3‘Gene Expression Analysis Arrays</code>这个条目下选择物种，再选择某种类型的芯片，如<code>Human Genome U95 Set</code>，其中<code>library</code>目录下的<code>Human Genome U95 Av2 Array</code>文件解压后含有<code>U95 Av2</code>即U95A第二版芯片的cdf文件；在<code>Current NetAffx Annotation Files</code>目录下含有最新版的注释文件。</p><blockquote><p><strong>Data Sheets中的说明文件（</strong><a href='http://www.affymetrix.com/support/technical/datasheets/hgu95_datasheet.pdf'>Human Genome U95 Set (pdf, 164 KB)）</a>注：U95 系列芯片不仅有A还有B，C，D，E这几种其他芯片，Affymetrix公司生产的芯片名称不同后缀有不同意义，如U95A代表U95这款芯片中的探针对应所有的已知基因（根据UniGene数据库的第95版设计的6000多个功能基因），而U95B～D代表这些芯片的探针还包括未知基因的EST序列设计的探针（根据dbEST/10-02-99数据库设计），后者用于发现新的功能基因，v2代表更新的第2版芯片</p></blockquote><p>解压下载的zip文件后，发现文件大小可能大了10倍，该注释文件为csv格式，有41列，常用数据库ID信息可以点<a href='http://www.biotrainee.com/forum.php?mod=viewthread&tid=411&page=1#pid3943'>这里</a></p><figure><table><thead><tr><th>列名</th><th>内容</th></tr></thead><tbody><tr><td>Probe Set ID</td><td>Affymerix探针的ID，CEL文件和CDF文件也使用该ID描述探针，其对应着某个基序列探针对，probe Set ID的<a href='http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.affx'>详细介绍</a>，每个Probe Set ID包括pm（完全匹配）和mm（错配），各自的10多个（16个）重复探针，所以每个芯片中一个Probe Set ID对应的探针序列种类为<span class="MathJax_Preview"></span><span class="MathJax_SVG" id="MathJax-Element-1-Frame" tabindex="-1" style="font-size: 100%; display: inline-block;"><svg xmlns:xlink="http://www.w3.org/1999/xlink" width="11.097ex" height="2.074ex" viewBox="0 -772.3 4778 892.8" role="img" focusable="false" style="vertical-align: -0.28ex;"><defs><path stroke-width="0" id="E1-MJMAIN-32" d="M109 429Q82 429 66 447T50 491Q50 562 103 614T235 666Q326 666 387 610T449 465Q449 422 429 383T381 315T301 241Q265 210 201 149L142 93L218 92Q375 92 385 97Q392 99 409 186V189H449V186Q448 183 436 95T421 3V0H50V19V31Q50 38 56 46T86 81Q115 113 136 137Q145 147 170 174T204 211T233 244T261 278T284 308T305 340T320 369T333 401T340 431T343 464Q343 527 309 573T212 619Q179 619 154 602T119 569T109 550Q109 549 114 549Q132 549 151 535T170 489Q170 464 154 447T109 429Z"></path><path stroke-width="0" id="E1-MJMAIN-2219" d="M55 251Q55 328 112 386T249 444T386 388T444 249Q444 171 388 113T250 55Q170 55 113 112T55 251Z"></path><path stroke-width="0" id="E1-MJMAIN-31" d="M213 578L200 573Q186 568 160 563T102 556H83V602H102Q149 604 189 617T245 641T273 663Q275 666 285 666Q294 666 302 660V361L303 61Q310 54 315 52T339 48T401 46H427V0H416Q395 3 257 3Q121 3 100 0H88V46H114Q136 46 152 46T177 47T193 50T201 52T207 57T213 61V578Z"></path><path stroke-width="0" id="E1-MJMAIN-36" d="M42 313Q42 476 123 571T303 666Q372 666 402 630T432 550Q432 525 418 510T379 495Q356 495 341 509T326 548Q326 592 373 601Q351 623 311 626Q240 626 194 566Q147 500 147 364L148 360Q153 366 156 373Q197 433 263 433H267Q313 433 348 414Q372 400 396 374T435 317Q456 268 456 210V192Q456 169 451 149Q440 90 387 34T253 -22Q225 -22 199 -14T143 16T92 75T56 172T42 313ZM257 397Q227 397 205 380T171 335T154 278T148 216Q148 133 160 97T198 39Q222 21 251 21Q302 21 329 59Q342 77 347 104T352 209Q352 289 347 316T329 361Q302 397 257 397Z"></path><path stroke-width="0" id="E1-MJMAIN-3D" d="M56 347Q56 360 70 367H707Q722 359 722 347Q722 336 708 328L390 327H72Q56 332 56 347ZM56 153Q56 168 72 173H708Q722 163 722 153Q722 140 707 133H70Q56 140 56 153Z"></path><path stroke-width="0" id="E1-MJMAIN-33" d="M127 463Q100 463 85 480T69 524Q69 579 117 622T233 665Q268 665 277 664Q351 652 390 611T430 522Q430 470 396 421T302 350L299 348Q299 347 308 345T337 336T375 315Q457 262 457 175Q457 96 395 37T238 -22Q158 -22 100 21T42 130Q42 158 60 175T105 193Q133 193 151 175T169 130Q169 119 166 110T159 94T148 82T136 74T126 70T118 67L114 66Q165 21 238 21Q293 21 321 74Q338 107 338 175V195Q338 290 274 322Q259 328 213 329L171 330L168 332Q166 335 166 348Q166 366 174 366Q202 366 232 371Q266 376 294 413T322 525V533Q322 590 287 612Q265 626 240 626Q208 626 181 615T143 592T132 580H135Q138 579 143 578T153 573T165 566T175 555T183 540T186 520Q186 498 172 481T127 463Z"></path></defs><g stroke="currentColor" fill="currentColor" stroke-width="0" transform="matrix(1 0 0 -1 0 0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-32" x="0" y="0"></use><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-2219" x="722" y="0"></use><g transform="translate(1444,0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-31"></use><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-36" x="500" y="0"></use></g><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-3D" x="2722" y="0"></use><g transform="translate(3778,0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-33"></use><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#E1-MJMAIN-32" x="500" y="0"></use></g></g></svg></span><script type="math/tex" id="MathJax-Element-1">2\bullet16=32</script>类，<code>geneNames(data_ALL1)[1:2]</code>结果为<code>[1] &quot;100_g_at&quot; &quot;1000_at&quot;</code>，<code>probeNames(data_ALL1)[1:32]</code>结果为这两种探针的重复</td></tr><tr><td>GeneChip array</td><td>芯片的型号，所有探针都为同一型号芯片，该列为多余列</td></tr><tr><td>Species Scientific Name</td><td>芯片对应基因的物种名称，所有探针对应的基因为同一物种</td></tr><tr><td>Annotaton Date</td><td>注释信息最后更新的时间，同一注释文件的所有探针更新为同一时间</td></tr><tr><td>Sequence Type</td><td>探针的序列类型，包括Consensus（保守）和Exemplar squences， A Consensus sequence is usually the result of a aligned cluster of EST sequences. An Exemplar sequence is a cluster that includes a representative sequence from each gene group, indicating a transcript was available at the time of design.  <strong>An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database.</strong></td></tr><tr><td>Sequence Source</td><td>通常是GenBank，也有少数是来自The Institute for Genomic Research</td></tr><tr><td>Transcript ID(Array Design)</td><td>为某个公共数据库序列ID号加上设计探针依据的序列类型，如X60957cds</td></tr><tr><td>Target Description.</td><td>序列的详细描述，包括类型</td></tr><tr><td><strong>Representative</strong> <strong>Public</strong> <strong>ID</strong></td><td>Genebank 或 Refseq数据库的ID</td></tr><tr><td>Archival UniGene Cluster.</td><td>在芯片设计时的Unigene ID号</td></tr><tr><td><strong>UniGene</strong> <strong>ID</strong></td><td>更新后（最新版本）的Unigene ID号</td></tr><tr><td>Genome Version.</td><td>序列比对时所用的基因组版本号</td></tr><tr><td><strong>Alignments</strong>.</td><td>靶基因在基因组上的位置，用碱基位置和带法表示如chr16:30125426-30134539 (-) // 93.03 // p11.2</td></tr><tr><td><strong>Gene Title.</strong></td><td>基因标题（来自Unigene或Entrez Gene 数据库）mitogen-activated protein kinase 3</td></tr><tr><td><strong>Gene</strong> <strong>Symbol</strong></td><td>基因名（来自Unigene或Entrez Gene数据库）如MAPK3</td></tr><tr><td><strong>Chromosomal Location.</strong></td><td>基因的位置，用细胞遗传学中的带法表示如：chr16p11.2</td></tr><tr><td>Unigene Cluster Type</td><td>表示Unigene序列的类型，包括full length，est或未知（---）</td></tr><tr><td><strong>Ensembl</strong></td><td>Ensembl数据库的编号</td></tr><tr><td><strong>Entrez Gene</strong></td><td>Entrz Gene数据库的编号，有Entrez ID的基因比没有的更具有可信，它们的信息更全，并且与其他多种数据库都建立了很好的连接</td></tr><tr><td>SwissProt.</td><td>对应的蛋白质在SwissProt数据库的ID</td></tr><tr><td>EC</td><td>EC数据库ID（很少看到，不太懂）</td></tr><tr><td><strong>OMIM</strong></td><td>Online Mendelian Inheritance in Man (OMIM) 数据库ID，基因相关的遗传病数据库</td></tr><tr><td>RefSeq Protein ID.</td><td>Genebank的蛋白相关保守序列ID</td></tr><tr><td><strong>RefSeq Transcript ID</strong></td><td>Genebank的mRNA类型的保守序列ID，通常与前面的<strong>Representative Public ID</strong> 重复</td></tr><tr><td>FlyBase</td><td>果蝇drosophila数据库对应的ID</td></tr><tr><td>AGI.</td><td>拟南芥Arabidopsis数据库ID</td></tr><tr><td>WormBase.</td><td>线虫C. elegans数据库对应的ID</td></tr><tr><td>MGI Name</td><td>小鼠mouse数据库对应的ID</td></tr><tr><td>RGD Name</td><td>大鼠rat数据库对应的ID</td></tr><tr><td>SGD accession number.</td><td>酵母saccharomyces数据库对应的ID</td></tr><tr><td>Gene Ontology Biological Process.</td><td>相关GO BP的ID和名称</td></tr><tr><td>Gene Ontology Cellular Component.</td><td>相关GO CC的ID和名称</td></tr><tr><td>Gene Ontology Molecular Function</td><td>相关GO MF的ID和名称</td></tr><tr><td>Pathway.</td><td>相关通路的名称</td></tr><tr><td>InterPro</td><td>一个蛋白质结构与数据库InterPro的ID</td></tr><tr><td>Trans Membrane</td><td>如果有已知跨膜结构域序列，则会注明</td></tr><tr><td>QTL.</td><td>大鼠基因连锁数据库RatMap提供与疾病连锁相关的信息，只有大鼠芯片才有</td></tr><tr><td>Annotation Description.</td><td>探针注释的方法，并且根据注释质量分为几个等级，<a href='https://www.affymetrix.com/support/help/IVT_glossary/index.affx'>A为最高等级</a></td></tr><tr><td>Annotation Transcript Cluster.</td><td>EntrezGene or UniGene transcript clusters available for the probe set. These records may represent families of transcripts and the strongest collection of evidence for a gene related to a probe set. After the accession, the number of matching probes is given in parentheses.（括号后是设计的探针种类数目</td></tr><tr><td>Transcript Assignments.</td><td>非常长的注释信息</td></tr><tr><td>Annotation Notes.</td><td>其他备注信息，包括Cross Hybridizing Probe Sets，Reverse Complement Probe Sets，Transcript Accessions的整合</td></tr></tbody></table></figure><h2><a name='header-n146' class='md-header-anchor '></a>3.3 GO（Gene Ontology）数据库</h2><blockquote><p>GO用有向无环图（DAG，directed acycilc graph）的形式，通过严格控制词汇对基因的功能进行描述</p></blockquote><h3><a name='header-n150' class='md-header-anchor '></a>3.3.1 基本组成</h3><p>GO数据库由两部分组成：</p><ol start='' ><li><p>GO注释（GOA），每个基因都有很多个功能的注释，每个功能代表了一个GO term，因此一个基因可能对应多个term如下所示HELLS蛋白对应的多个GO term（也可以在官网查找：<a href='http://amigo.geneontology.org/amigo/search/annotation?q=*:*&fq=bioentity:%22UniProtKB:Q9NRZ9%22' target='_blank' class='url'>http://amigo.geneontology.org/amigo/search/annotation?q=*:*&fq=bioentity:%22UniProtKB:Q9NRZ9%22</a>），其下载入口为：<a href='http://www.geneontology.org/page/download-go-annotations' target='_blank' class='url'>http://www.geneontology.org/page/download-go-annotations</a>【<code>注意第3~5行都是同一个GO term，GO:000551，但是其PMID不同，也就是参考的文献不同（一般都是高通量实验文章</code>）】</p><pre class="md-fences md-end-block" lang="" style="break-inside: unset;"> <div class="CodeMirror cm-s-inner CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 4px; left: 4px;"></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0000775<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>C<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0004386<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000037<span class="cm-tab" role="presentation" cm-text="	">  </span>IEA<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB-KW:KW-0347<span class="cm-tab" role="presentation" cm-text="	">    </span>F<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180324<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0005515<span class="cm-tab" role="presentation" cm-text="	">  </span>PMID:17314511<span class="cm-tab" role="presentation" cm-text="	">   </span>IPI<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:P01106<span class="cm-tab" role="presentation" cm-text="	">    </span>F<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180326<span class="cm-tab" role="presentation" cm-text="	">    </span>IntAct</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0005515<span class="cm-tab" role="presentation" cm-text="	">  </span>PMID:17353931<span class="cm-tab" role="presentation" cm-text="	">   </span>IPI<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:P01106<span class="cm-tab" role="presentation" cm-text="	">    </span>F<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180326<span class="cm-tab" role="presentation" cm-text="	">    </span>IntAct</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0005515<span class="cm-tab" role="presentation" cm-text="	">  </span>PMID:22157815<span class="cm-tab" role="presentation" cm-text="	">   </span>IPI<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:O00716<span class="cm-tab" role="presentation" cm-text="	">    </span>F<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180326<span class="cm-tab" role="presentation" cm-text="	">    </span>IntAct</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0005524<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000037<span class="cm-tab" role="presentation" cm-text="	">  </span>IEA<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB-KW:KW-0067<span class="cm-tab" role="presentation" cm-text="	">    </span>F<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180324<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0005634<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000039<span class="cm-tab" role="presentation" cm-text="	">  </span>IEA<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB-SubCell:SL-0191<span class="cm-tab" role="presentation" cm-text="	">   </span>C<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180324<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0005721<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>C<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0006346<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0006351<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000037<span class="cm-tab" role="presentation" cm-text="	">  </span>IEA<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB-KW:KW-0804<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180324<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0007049<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000037<span class="cm-tab" role="presentation" cm-text="	">  </span>IEA<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB-KW:KW-0131<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180324<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0007275<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0010216<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0031508<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0046651<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000024<span class="cm-tab" role="presentation" cm-text="	">  </span>ISS<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB:Q60848<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20061106<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">UniProtKB<span class="cm-tab" role="presentation" cm-text="	">   </span>Q9NRZ9<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS<span class="cm-tab" role="presentation" cm-text="	">   </span><span class="cm-tab" role="presentation" cm-text="	">    </span>GO:0051301<span class="cm-tab" role="presentation" cm-text="	">  </span>GO_REF:0000037<span class="cm-tab" role="presentation" cm-text="	">  </span>IEA<span class="cm-tab" role="presentation" cm-text="	"> </span>UniProtKB-KW:KW-0132<span class="cm-tab" role="presentation" cm-text="	">    </span>P<span class="cm-tab" role="presentation" cm-text="	">   </span>Lymphoid-specific helicase<span class="cm-tab" role="presentation" cm-text="	">  </span>HELLS_HUMAN|HELLS|PASG|SMARCA6|Nbla10143<span class="cm-tab" role="presentation" cm-text="	">    </span>protein<span class="cm-tab" role="presentation" cm-text="	"> </span>taxon:9606<span class="cm-tab" role="presentation" cm-text="	">  </span>20180324<span class="cm-tab" role="presentation" cm-text="	">    </span>UniProt</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; border-bottom: 0px solid transparent; top: 1096px;"></div><div class="CodeMirror-gutters" style="display: none; height: 1126px;"></div></div></div></pre><p>​</p></li><li><p>Gene Ontology提供了各种生物学功能（GO term）的层次关系，用DAG表示，由Gene Ontology委员会维护，描述基因的功能及功能之间的联系，从以下三个方面（GO term的三个类别）来对基因功能进行描述：</p><ul><li>Biological process (what)</li><li>Molecular function（how）</li><li>Cellular component （where）</li></ul><p>因此共有3个Ontology，这三个分别为各个Ontology的level 1 term，level越高，其描述的功能越具体详细<br/></p><p>其下载入口为：&lt;<a href='http://geneontology.org/page/download-ontology' target='_blank' class='url'>http://geneontology.org/page/download-ontology</a>  <br/></p><p>更加直观的显示入口：<a href='http://amigo.geneontology.org/amigo/dd_browse' target='_blank' class='url'>http://amigo.geneontology.org/amigo/dd_browse</a><br/>
查看某个term包含的基因：<a href='http://amigo.geneontology.org/amigo/term/GO:0005515' target='_blank' class='url'>http://amigo.geneontology.org/amigo/term/GO:0005515</a>  <br/></p><p>可视化入口：<a href='http://amigo.geneontology.org/visualize' target='_blank' class='url'>http://amigo.geneontology.org/visualize</a>或<a href='http://amigo1.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006346' target='_blank' class='url'>http://amigo1.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006346</a>如：输入<code>{&quot;GO:0006346&quot;:{ &quot;fill&quot;:  &quot;blue&quot;}}</code>，结果如下：越往下走level数越高，功能越具体<br/></p><p><img src='assets\visualize.png' alt='' referrerPolicy='no-referrer' /></p><p>各GO terms的关系有两种，一是is_a（表特殊情况，Subclass），二是part_of（表组成部分，Membership）【5_prime_UTR is part_of a transcript, and mRNA is_a kind of transcript 】。在对基因进行GO注释时，注释在高level下的基因同时也能注释在该term的母节点上</p><h3><a name='header-n186' class='md-header-anchor '></a>3.3.2 证据的级别</h3><p>证据质量的级别可以分为6个：</p><ol start='' ><li>IDA， TAS</li><li>IMP，IPI，IGI</li><li>ISS，IEP</li><li>NAS</li><li>IEA</li><li>IC</li></ol><figure><table><thead><tr><th>证据代码</th><th>详细内容</th></tr></thead><tbody><tr><td><strong>IDA</strong>（inferred from direct assay）</td><td>有文献通过实验直接证明的功能</td></tr><tr><td><strong>TAS</strong>（traceable author statement）</td><td>综述或教科书中的描述，并且有相应参考文献</td></tr><tr><td><em>IMP</em>（inferred from mutant phenotype）</td><td>突变实验（敲除或敲降）证明</td></tr><tr><td><em>IPI</em>（inferred from physical interaction）</td><td>免疫共沉淀等方法证明有物理结合</td></tr><tr><td><em>IGI</em>（inferred from genetic interaction）</td><td>从协同致死作用或互补及抑制的遗传学实验证明</td></tr><tr><td>ISS（inferred from sequence or structure similarity）</td><td>通过Blast比对推测，被综述提及</td></tr><tr><td>IEP（inferred from expression pattern）</td><td>通过Norther，Western或芯片实验表明其表达的时期和部位信息</td></tr><tr><td><em>NAS</em>（non-traceable author statement）</td><td>在文章摘要，背景或讨论部分出现，但是没有原始引用</td></tr><tr><td>IEA（inferred from electronic annotation）</td><td>根据序列相似性推测，但是没有被综述提及</td></tr><tr><td>IC（inferred by curator）</td><td>仅仅是根据某种理由推测（如某物质存在与核内，推测其具有转录因子功能）</td></tr><tr><td>ND（no biological data available）</td><td>nly used for annotations to ”unknown”</td></tr><tr><td>NR （not recorded）</td><td>used only for annotations created before curators started adding evidence codes</td></tr></tbody></table></figure><h3><a name='header-n248' class='md-header-anchor '></a>3.4 使用Gominer做GO富集分析（已经放弃，软件总是运行不了）</h3><ol start='' ><li><p>安装<a href='https://www.mysql.com/'>mysql数据库</a>，并设置root密码为root</p></li><li><p>设置好环境变量后，在命令行输入<code>mysql -uroot -proot</code>进入mysql界面</p></li><li><p>在mysql中创建goDb数据库：</p><pre class="md-fences md-end-block" lang=""> <div class="CodeMirror cm-s-inner CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 4px; left: 4px;"></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><span><span>​</span>x</span></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">create database IF NOT EXISTS goDb;</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">grant ALL on *.* to 'root'@%  identified by 'root；</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; border-bottom: 0px solid transparent; top: 59px;"></div><div class="CodeMirror-gutters" style="display: none; height: 89px;"></div></div></div></pre><p>​</p></li><li><p>下载go数据库文件：<a href='http://archive.geneontology.org/' target='_blank' class='url'>http://archive.geneontology.org/</a>，<strong>go_daily-termdb-tables.tar.gz </strong>，解压到go数据目录（自己创建的存放go数据文件的目录，如goData），并在goData目录下，创建loadDB.bat文件，文件内容如下：</p></li></ol><pre class="md-fences md-end-block" lang="bash"> <div class="CodeMirror cm-s-inner CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 4px; left: 4px;"></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-keyword">for</span> %%a <span class="cm-keyword">in</span> (%1\*.sql) <span class="cm-keyword">do</span> type %%a | mysql <span class="cm-attribute">-u</span>%2 <span class="cm-attribute">-p</span>%3 <span class="cm-attribute">-D</span>%4</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-keyword">for</span> %%b <span class="cm-keyword">in</span> (%1\*.txt) <span class="cm-keyword">do</span> mysqlimport <span class="cm-attribute">-L</span> <span class="cm-attribute">-u</span>%2 <span class="cm-attribute">-p</span>%3 %4 %%b</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; border-bottom: 0px solid transparent; top: 42px;"></div><div class="CodeMirror-gutters" style="display: none; height: 72px;"></div></div></div></pre><p>​</p><ol start='5' ><li>在goData目录打开命令行，输入以下命令完成写入数据库操作</li></ol><pre class="md-fences md-end-block" lang=""> <div class="CodeMirror cm-s-inner CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 4px; left: 4px;"></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">.\loadDB.bat . root root goDb</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; border-bottom: 0px solid transparent; top: 25px;"></div><div class="CodeMirror-gutters" style="display: none; height: 55px;"></div></div></div></pre><p>​</p><ol start='6' ><li>打开Gominer.jar文件，进入图形界面，【file】-【Load GO Terms】，</li></ol><pre class="md-fences md-end-block" lang=""> <div class="CodeMirror cm-s-inner CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 4px; left: 4px;"></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">jdbc:mysql://10.10.23.200（我的电脑IP）:3306/goDb</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">jdbc:mysql://localhost:3306/goDb</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">root</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; border-bottom: 0px solid transparent; top: 59px;"></div><div class="CodeMirror-gutters" style="display: none; height: 89px;"></div></div></div></pre></li></ol><p>&nbsp;</p><p>&nbsp;</p></div>
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